A Zero-Knowledge Based Introduction to Biology

Konstantinos (Gus) Katsiapis25 Sep 2009

Thanks to Cory McLean and George Asimenos

Cells: Building Blocks of Life

© 1997-2005 Coriell Institute for Medical Research

cell, membrane, cytoplasm, nucleus, mitochondrion

2

DNA: “Blueprints” for a cell

• Genetic information encoded in long strings of double-stranded DNA

• DeoxyriboNucleic Acid comes in only four flavors: Adenine, Cytosine, Guanine, Thymine

3

Nucleotide

O

C C

CC

H

H

HHH

H

H

COPO

O-

O

to next nucleotide

to previous nucleotide

to base

deoxyribose, nucleotide, base, purine (A,G), pyrimidine (T,C), 3’, 5’

3’

5’ Adenine (A)

Cytosine (C)

Guanine (G)

Thymine (T)

Let’s write “AGACC”!

pyrimidines

purines

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“AGACC” (backbone)

5

“AGACC” (DNA)deoxyribonucleic acid (DNA)

5’

5’3’

3’

6

DNA is double stranded

3’

5’

5’

3’

DNA is always written 5’ to 3’

AGACC or GGTCT

strand, reverse, complement, reverse-complement

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DNA Packaginghistone, nucleosome, chromatin, chromosome, centromere, telomere

H1DNA

H2A, H2B, H3, H4

~146bp

telomerecentromere nucleosome

chromatin

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The Genome

The genome is the full set of hereditary information for an organism

Humans bundle two copies of the genome into 46 chromosomes in every cell= 2 * (1-22 + X/Y)

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Building an Organism

cellDNA Every cell has the same sequence of

DNA

Subsets of the DNA sequence determine the identity and function of different cells

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From DNA To Organism

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Proteins do most of the work in biology, and are encoded by subsequences of DNA, known as genes.

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RNA

O

C C

CC

H

OH

HHH

H

H

COPO

O-

O

to next ribonucleotide

to previous ribonucleotide

to base

ribose, ribonucleotide, U

3’

5’ Adenine (A)

Cytosine (C)

Guanine (G)

Uracil (U)

pyrimidines

purines

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T U

Genes & Proteins

3’5’

5’3’ TAGGATCGACTATATGGGATTACAAAGCATTTAGGGA...TCACCCTCTCTAGACTAGCATC

ATCCTAGCTGATATACCCTAATGTTTCGTAAATCCCT...AGTGGGAGAGATCTGATCGTAG

AUGGGAUUACAAAGCAUUUAGGGA...UCACCCUCUCUAGACUAGCAUC

(transcription)

(translation)

Single-stranded RNA

protein

Double-stranded DNA

gene, transcription, translation, protein

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Gene Transcriptionpromoter

3’5’

5’3’

G A T T A C A . . .

C T A A T G T . . .

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Promoter: A region of DNA facilitating transcription of a gene. Usually located one the same strand, upstream and nearby.

Gene Transcriptiontranscription factor, binding site, RNA polymerase

3’5’

5’3’

Transcription factors: a type of protein that binds to DNA and helps initiate gene transcription.

Transcription factor binding sites: Short sequences of DNA (6-20 bp) recognized and bound by TFs.

RNA polymerase binds a complex of TFs in the promoter.

G A T T A C A . . .

C T A A T G T . . .

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Gene Transcription

3’5’

5’3’

The two strands are separated

G A T T A C A . . .

C T A A T G T . . .

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Gene Transcription

3’5’

5’3’

An RNA copy of the 5’→3’ sequence is created from the 3’→5’ template

G A T T A C A . . .

C T A A T G T . . .

G A U U A C A

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Gene Transcription

3’5’

5’3’

G A U U A C A . . .

G A T T A C A . . .

C T A A T G T . . .

pre-mRNA 5’ 3’

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RNA Processing5’ cap, polyadenylation, exon, intron, splicing, UTR, mRNA

5’ cap poly(A) tail

intron

exon

mRNA

5’ UTR 3’ UTR

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Gene Structure

5’ 3’

promoter5’ UTR exons 3’ UTR

introns

codingnon-coding

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How many?(Human Genome)

• Exons per gene:~ 8 on average (max: 148)

• Nucleotides per exon:170 on average (max: 12k)

• Nucleotides per intron:5,500 on average (max: 500k)

• Nucleotides per gene:45k on average (max: 2,2M)

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From RNA to Protein

• Proteins are long strings of amino acids joined by peptide bonds

• Translation from RNA sequence to amino acid sequence performed by ribosomes

• 20 amino acids 3 RNA letters required to specify a single amino acid

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Amino acidamino acid

C

O

N

H

C

H

H OH

R

There are 20 standard amino acids

AlanineArginine

AsparagineAspartateCysteine

GlutamateGlutamine

GlycineHistidine

IsoleucineLeucineLysine

MethioninePhenylalanine

ProlineSerine

ThreonineTryptophan

TyrosineValine

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C

O

N

H

C

H

R

to previous aa to next aa

N-terminus

(start)

H OH

C-terminus

(end)

N-terminus, C-terminus

from 5’ 3’ mRNA24

Proteins

Translation

The ribosome (a complex of protein and RNA) synthesizes a protein by reading the mRNA in triplets (codons). Each codon is translated to an amino acid.

ribosome, codon

mRNA

P site A site

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Translation

GGGG GlyGAG GluGCG AlaGUG Val

A GGA GlyGAA Glutamic acid (Glu)

GCA AlaGUA Val

C GGC GlyGAC AspGCC AlaGUC Val

U GGU Glycine (Gly)GAU Aspartic acid (Asp)

GCU Alanine (Ala)GUU Valine (Val)

G

GAGG Arg AAG LysACG ThrAUG Methionine (Met) or START

A AGA Arginine (Arg)AAA Lysine (Lys)ACA Thr AUA Ile

C AGC Ser AAC AsnACC ThrAUC Ile

U AGU Serine (Ser)AAU Asparagine (Asn)ACU Threonine (Thr)

AUU Isoleucine (Ile)

A

GCGG Arg CAG GlnCCG ProCUG Leu

A CGA Arg CAA Glutamine (Gln)CCA ProCUA Leu

C CGC Arg CAC HisCCC ProCUC Leu

U CGU Arginine (Arg)CAU Histidine (His)CCU Proline (Pro)CUU Leucine (Leu)

C

GUGG Tryptophan (Trp)

UAG STOPUCG Ser UUG Leu

A UGA STOPUAA STOPUCA Ser UUA Leucine (Leu)

C UGC CysUAC TyrUCC SerUUC Phe

U UGU Cysteine (Cys)UAU Tyrosine (Tyr)UCU Serine (Ser)UUU Phenylalanine (Phe)

U

GACU

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Translation

5’ . . . A U U A U G G C C U G G A C U U G A . . . 3’

UTR Met

Start Codon

Ala Trp ThrStop

Codon27

Translation

Met Ala

5’ . . . A U U A U G G C C U G G A C U U G A . . . 3’

Trp

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Transcription and Translation [3D Simulation]

Errors?

• What if the transcription / translation machinery makes mistakes?

• What is the effect of mutations in coding regions?

mutation

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Reading Framesreading frame

G C U U G U U U A C G A A U U A G

G C U U G U U U A C G A A U U A G

G C U U G U U U A C G A A U U A G

G C U U G U U U A C G A A U U A G

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Synonymous Mutation

G C U U G U U U A C G A A U U A G

Ala Cys Leu Arg Ile

G C U U G U U U A C G A A U U A G

synonymous (silent) mutation, fourfold siteG

G C U U G U U U G C G A A U U A G

Ala Cys Leu Arg Ile

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Missense Mutation

G C U U G U U U A C G A A U U A G

Ala Cys Leu Arg Ile

G C U U G U U U A C G A A U U A G

missense mutationG

G C U U G G U U A C G A A U U A G

Ala Trp Leu Arg Ile

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Nonsense Mutation

G C U U G U U U A C G A A U U A G

Ala Cys Leu Arg Ile

G C U U G U U U A C G A A U U A G

nonsense mutationA

G C U U G A U U A C G A A U U A G

Ala STOP

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Frameshift

G C U U G U U U A C G A A U U A G

Ala Cys Leu Arg Ile

G C U U G U U U A C G A A U U A G

frameshift

G C U U G U U A C G A A U U A G

Ala Cys Tyr Glu Leu

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Gene Expression Regulation

• When should each gene be expressed?• Regulate gene expression

Examples:

– Make more of gene A when substance X is present– Stop making gene B once you have enough– Make genes C1, C2, C3 simultaneously

• Why? Every cell has same DNA but each cell expresses different proteins.

• Signal transduction: One signal converted to another– Cascade has “master regulators” turning on many

proteins, which in turn each turn on many proteins, ...

Regulation, signal transduction

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Gene Regulation

Gene expression is controlled at many levels: DNA chromatin structure Transcription Post-transcriptional modification RNA transport Translation mRNA degradation Post-translational modification

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Transcription Regulation

• Much gene regulation occurs at the level of transcription.

• Primary players:– Binding sites (BS) in cis-regulatory

modules (CRMs)

– Transcription factor (TF) proteins

– RNA polymerase II

• Primary mechanism: – TFs link to BSs

– Complex of TFs forms

– Complex assists or inhibits formation of the RNA polymerase II machinery

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Tx Factor Binding Sites

• Short, degenerate DNA sequences recognized by particular TFs

• For complex organisms, cooperative binding of multiple TFs required to initiate transcription

Binding Sequence Logo

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Transcription Regulation Mechanisms

enhancer, silencer, insulator

Transcription Factor Specificity:

Enhancer:

Silencer:

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Insulator:

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unicellular

multicellular

Unicellular vs. Multicellular

Non-coding RNAs

• RNAs transcribed from DNA but not translated into protein

• Structural ncRNAs: Conserved secondary structure (A-U, C-G, G-U)

• Involved in gene regulation

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Summary

• All hereditary information encoded in double-stranded DNA

• Each cell in an organism has same DNA

• DNA RNA protein• Proteins have many diverse roles in

cell• Gene regulation diversifies protein

products within different cells42

The end?

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